PredGly

Installation

Because the program is written in Python 2.7, python 2.7 with the pip tool must be installed first. Glycation uses the following dependencies: numpy, pandas, matplotlib, scipy and scikit-learn. You can install these packages first, by the following commands:

If you meet an error after inputting above commands in Linux, the specific contents are as follows:
Could not install packages due to an EnvironmentError: [Errno 13] Permission denied: '/usr/local/lib/python2.7/dist-packages/sklearn'
Consider using the '--user' option or check the permissions.
Users can change the commands into:

Running PredGly

open cmd in Windows or terminal in Linux, then cd to the PredGly-master/codes folder which contains predict.py
For general glycation site prediction using our model, run:python predict.py -input [custom predicting data in txt format] -threshold [threshold value] -output [ predicting results in csv format]

Example:python predict.py -input ../codes/example.txt -threshold 0.5 -output ../codes/results.csv-output is optional parameter, while -input and -threshold are required parameters. Prediction results will show in the cmd or terminal, and if you don't want to save results, you need not input -output.

Example:python predict.py -input ../codes/example.txt -threshold 0.5

For details of -input,-threshold and -output, run:python predict.py -h

Announcements

In order to obtain the prediction results, please save the query protein sequences and protein name in txt format. Users can refer to the example.txt under the codes folder. Also of note, each protein name should be added by '>', otherwise the program will not occur error.